tbuckley/cabot-search huggingface dataset:
Increasing melanoma incidence and survival trend shifts with improved melanoma-specific survival between 1990 and 2020 in Sweden
Authors: Sofi Vikström, Rasmus Mikiver, Jan Lapins, Kari Nielsen, Ismini Vassilaki, Johan Lyth, Karolin Isaksson, Hanna Eriksson
Journal: British Journal of Dermatology (2023)

Abstract Background Melanoma-specific survival (MSS) is heterogenous between stages and is highly dependent on the T stage for primary localized disease. New systemic therapies for metastatic cutaneous melanoma (CM) have been introduced since 2012 in Sweden. Objectives To analyse the incidence and MSS time trends between 1990 and 2020 in Sweden. Methods Nationwide, population-based and prospectively collected clinico-pathological data on invasive CM from the Swedish Melanoma Registry (SweMR) were analysed for survival trends between 1990 and 2020 using Kaplan–Meier curves and Cox proportional hazard ratios (HRs). Results In total, 77 036 primary invasive CMs were diagnosed in 70 511 patients in Sweden between 1990 and 2020. The 5-year MSS [95% confidence interval (CI)] was 88.9% (88.3–89.4) for 1990–2000, 89.2% (88.7–89.6) for 2001–2010 and 93.0% (92.7–93.9) for 2011–2020. The odds ratios for being diagnosed with nodular melanoma (vs. superficial spreading melanoma) was significantly reduced by 20% (2001–2010) and by 46% (2011–2020) vs. the reference period 1990–2000. Overall, the MSS improved over both diagnostic periods (2001–2010 and 2011–2020) vs. the reference period 1990–2000 among men and women, respectively [HRmen: 2001–2010: 0.89 (95% CI 0.82–0.96) and 2011–2020: 0.62 (95% CI 0.56–0.67); HRwomen: 2001–2010: 0.82 (95% CI 0.74–0.91) and 2011–2020: 0.62 (95% CI 0.56–0.70)]. The risk of death from CM was significantly lower in all age groups for both men and women in the most recent diagnostic period (2011–2020 vs.1990–2000). Conclusions The results emphasize the improved MSS among men and women in Sweden. The MSS improvements, specifically for the period 2011–2020, may be correlated to the introduction of new systemic therapies and are here shown for the first time in detail for Sweden.
Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses
Authors: Abayomi S Olabode, Mitchell J Mumby, Tristan A Wild, Laura Muñoz-Baena, Jimmy D Dikeakos, Art F Y Poon
Journal: Molecular Biology and Evolution (2023)

Abstract Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss
Authors: Jessica M Warren, Amanda K Broz, Ana Martinez-Hottovy, Christian Elowsky, Alan C Christensen, Daniel B Sloan
Journal: Molecular Biology and Evolution (2023)

Abstract The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.
Validity, reliability, responsiveness and interpretability of the Recap of atopic eczema (RECAP) questionnaire
Authors: Junfen Zhang, Aviël Ragamin, Geertruida L E Romeijn, Laura Loman, Jart A F Oosterhaven, Marie L A Schuttelaar
Journal: British Journal of Dermatology (2023)

Limited research has been conducted on the measurement properties of the Recap of atopic eczema (RECAP) questionnaire, particularly in relation to interpretability.To investigate the validity, reliability, responsiveness and interpretability of the Dutch RECAP in adults with atopic dermatitis (AD).We conducted a prospective study in a Dutch tertiary hospital, recruiting adults with AD between June 2021 and December 2022. Patients completed the RECAP questionnaire, reference instruments and anchor questions at the following three timepoints: baseline, after 1-3 days and after 4-12 weeks. Hypotheses testing was used to investigate single-score validity and change-score validity (responsiveness). To assess reliability, both standard error of measurement (SEMagreement) and intraclass correlation coefficient (ICCagreement) were reported. To assess the interpretability of single scores, bands for eczema control were proposed. To investigate the interpretability of change scores, both smallest detectable change (SDC) and minimally important change (MIC) scores were determined. To estimate the MIC scores, four different anchor-based methods were employed: the mean change method, 95% limit cut-off point, receiver operating characteristic curve and predictive modelling.In total, 200 participants were included (57.5% male sex, mean age 38.5 years). Of the a priori hypotheses, 82% (single-score validity) and 59% (responsiveness) were confirmed. Known-group analyses showed differences in the RECAP scores between patient groups based on disease severity and impairment of the quality of life. The SEMagreement was 1.17 points and the ICCagreement was 0.988. The final banding was as follows: 0-1 (completely controlled); 2-5 (mostly controlled); 6-11 (moderately controlled); 12-19 (a little controlled); 20-28 (not at all controlled). Moreover, a single cut-off point of ≥ 6 was determined to identify patients whose AD is not under control. The SDC was 3.2 points, and the MIC value from the predictive modelling was 3.9 points. Neither floor nor ceiling effects were observed.The RECAP has good single-score validity, moderate responsiveness and excellent reliability. This study fills a gap in the interpretability of the RECAP. Our results indicate a threshold of ≥ 6 points to identify patients whose AD is 'not under control', while an improvement of ≥ 4 points represents a clinically important change. Given its endorsement by the Harmonising Outcome Measures for Eczema initiatives, the results of this study support the integration of RECAP into both routine clinical practice and research settings.
Increased risk of depression in patients with discoid lupus erythematosus: a nested, case–control study in the <i>All of Us</i> Research Program
Authors: Gloria F Chen, Katharina S Shaw, Stephanie Sanchez-Melendez, Ruth Ann Vleugels, Jeffrey M Cohen
Journal: British Journal of Dermatology (2023)

In this nested case–control study, we found a twofold increased risk of major depressive disorder in patients with discoid lupus erythematosus (DLE) vs. controls without DLE, using the All of Us database, a National Institutes of Health (USA) research programme that prioritizes recruitment from demographic groups under-represented in biomedical research. This is the first large-scale study of this association in a heterogeneous population and highlights the importance vigilance regarding the increased risk of depression in patients with DLE.
Dual-process moral judgment beyond fast and slow
Authors: Joshua D. Greene
Journal: Behavioral and Brain Sciences (2023)

Abstract De Neys makes a compelling case that the sacrificial moral dilemmas do not elicit competing “fast and slow” processes. But are there even two processes? Or just two intuitions? There remains strong evidence, most notably from lesion studies, that sacrificial dilemmas engage distinct cognitive processes generating conflicting emotional and rational responses. The dual-process theory gets much right, but needs revision.
Fast and slow language processing: A window into dual-process models of cognition
Authors: Fernanda Ferreira, Falk Huettig
Journal: Behavioral and Brain Sciences (2023)

Abstract Our understanding of dual-process models of cognition may benefit from a consideration of language processing, as language comprehension involves fast and slow processes analogous to those used for reasoning. More specifically, De Neys's criticisms of the exclusivity assumption and the fast-to-slow switch mechanism are consistent with findings from the literature on the construction and revision of linguistic interpretations.
Not feeling right about uncertainty monitoring
Authors: Ian R Newman, Valerie A Thompson
Journal: Behavioral and Brain Sciences (2023)

Abstract De Neys proposed a “switch” model to address what he argued to be lacuna in dual-process theory, in which he theorized about the processes that initiate and terminate analytic thinking. We will argue that the author neglected to acknowledge the abundant literature on metacognitive functions, specifically, the meta-reasoning framework developed by Ackerman and Thompson (2017), that addresses just those questions.
A commentary on ‘Clinical outcomes and quality of life after contemporary isolated coronary bypass grafting: a prospective cohort study’
Authors: Tiangang Zhou, Yidan Wang, Guoying Wang, Qingwei Liu, Zhiming Jiang
Journal: International Journal of Surgery (2023)

Zhou, Tiangang MD; Wang, Yidan MD; Wang, Guoying MD; Liu, Qingwei MD; Jiang, Zhiming MD Author Information
Architecture‐Engineered Electrospinning Cascade Regulates Spinal Microenvironment to Promote Nerve Regeneration
Authors: Yu Tang, Zonghan Xu, Jincheng Tang, Yichang Xu, Ziang Li, Wenbo Wang, Liang Wu, Kun Xi, Yong Gu, Liang Chen
Journal: Advanced Healthcare Materials (2023)

Adv. Healthcare Mater. 2023, 12, 2202658 https://doi.org/10.1002/adhm.202202658 After initial online publication, several errors were found regarding the data in some of the figures. 1. Corrections Related to Figure 1 In Figure 1D, for the MS@G/S column, the wt% values of the chemical elements are incorrect. The correct Figure 1 is shown below: As a consequence of this correction to Figure 1, in the sub-section "2.2. Production of the Directional MS Electrospun Scaffold withGelMA Coating Technology", the sentence "in the MS@G group, wt% of C, N, and O were 55.3%, 44.7%, and 8.1%, respectively." should read "in the MS@G group, wt% of C, N, and O were 54.1%, 8.1%, and 37.8%, respectively." 2. Corrections Related to Figure 2 In Figure 2C, a numerical error in calculating the Young's modulus led to the y-axis numbers being incorrect by a factor of 100. The correct Figure 2 is shown below: As a consequence of this correction to Figure 2, in the sub-section "2.2. Production of the Directional MS Electrospun Scaffold withGelMA Coating Technology", the sentence "In the MS group, the HA core–shell structure sacrificed tensile strength to a certain extent, with Young's modulus being 0.380 ± 0.015 MPa. However, in the MS@G/S group, the GelMA coating led to a slightly lower maximum tensile strength than the PLA fiber and Young's modulus of 0.50 ± 0.010 MPa." should read "In the MS group, the HA core–shell structure sacrificed tensile strength to a certain extent, with Young's modulus being 38 ± 1.5 MPa. However, in the MS@G/S group, the GelMA coat- ing led to a slightly lower maximum tensile strength than the PLA fiber and Young's modulus of 50 ±1.0 MPa." 3. Corrections Related to Figure 7 In Figure 7B, the values of the BBB score (y-axis) are incorrect. The correct Figure 7 is shown below: 4. Other Corrections In section "2.4. Biocompatibility and Adhesion", the sentence "[…] as observed by TEM (Figure S2B, Supporting Information)." should read "[…] as observed by SEM (Figure 2SB, Supporting Information)." The corrections to these figures and text do not affect the overall results and conclusions of this work. The authors apologize for any inconvenience caused.
Brown Adipose Tissue and BMP3b Decrease Injury in Cardiac Ischemia-Reperfusion
Authors: Íngrid Martí-Pàmies, Robrecht Thoonen, Michael Morley, Lauren Graves, Jesus Tamez, Alex Caplan, Kendra McDaid, Vincent Yao, Allyson Hindle, Robert E. Gerszten, Laurie A. Farrell, Li Li, Yu-Hua Tseng, Gerson Profeta, Emmanuel S. Buys, Donald B. Bloch, Marielle Scherrer-Crosbie
Journal: Circulation Research (2023)

Despite advances in treatment, myocardial infarction (MI) is a leading cause of heart failure and death worldwide, with both ischemia and reperfusion (I/R) causing cardiac injury. A previous study using a mouse model of nonreperfused MI showed activation of brown adipose tissue (BAT). Recent studies showed that molecules secreted by BAT target the heart. We investigated whether BAT attenuates cardiac injury in I/R and sought to identify potential cardioprotective proteins secreted by BAT.
Mussel‐Derived Bioadaptive Artificial Tendon Facilitates the Cell Proliferation and Tenogenesis to Promote Tendon Functional Reconstruction
Authors: Xiaoyan Wang, Kaige Xu, Lan Mu, Xiaoqi Zhang, Guangtao Huang, Malcolm Xing, Zhibin Li, Jun Wu
Journal: Advanced Healthcare Materials (2023)

Tendon injuries range from acute-related trauma to chronic-related injuries are prevalent and bring substantial pain, functional loss, and even disability to the patients. The management of tendon injuries is tricky due to the innate limited regenerative capability of the tendon. Currently, surgical intervention of tendon injuries with artificial tendons remains the standard of care. However, most of artificial tendons are manufactured with synthetic materials, which possess relatively poor biomimetic characteristics and inadequate inherent biodegradability, hence rendering limited cell proliferation and migration for tendon healing. To address these limitations, this work develops a mussel-derived artificial tendon based on double-cross-linked chitosan modification. In this design, decellularized artificial tendon serves as a natural biomimetic scaffold to facilitate the migration and adhesion of tendon repair cells. Additionally, as the cells proliferate, the artificial tendon can be degraded to facilitate tendon regeneration. Moreover, the chitosan cross-linking further enhances the mechanical strength of artificial tendon and offers a controllable degradation. The in vitro and in vivo experimental results demonstrate that mussel-derived artificial tendon not only accelerate the tendon functional reconstruction but also enable harmless clearance at postimplantation. The finding provides a promising alternative to conventional artificial tendons and spurs a new frontier to explore nature-derived artificial tendons.
“Switching” between fast and slow processes is just reward-based branching
Authors: George Ainslie
Journal: Behavioral and Brain Sciences (2023)

Abstract Shortcuts to goals are rewarded by faster attainment and punished by more frequent failure, so selection of the various kinds – heuristics, cached sequences (habits or macros ), gut instincts – depends on reward history just like other kinds of choice. The speeds of shortcuts lie on continua along with speeds of deliberation, and these continua have no obvious separation points.
Switching: Cultural fluency sustains and cultural disfluency disrupts thinking fast
Authors: Daphna Oyserman
Journal: Behavioral and Brain Sciences (2023)

Abstract Culture-as-situated cognition theory provides insight into the system 1 monitoring algorithm. Culture provides people with an organizing framework, facilitating predictions, focusing attention, and providing experiential signals of certainty and uncertainty as system 1 inputs. When culture-based signals convey that something is amiss, system 2 reasoning is triggered and engaged when resources allow; otherwise, system 1 reasoning dominates.
Dual Photo‐Enhanced Interpenetrating Network Hydrogel with Biophysical and Biochemical Signals for Infected Bone Defect Healing
Authors: Guangyu Jian, Dize Li, Qiwei Ying, Xu Chen, Qiming Zhai, Si Wang, Li Mei, Richard D. Cannon, Ping Ji, Wenzhao Liu, Huanan Wang, Tao Chen
Journal: Advanced Healthcare Materials (2023)

The healing of infected bone defects (IBD) is a complex physiological process involving a series of spatially and temporally overlapping events, including pathogen clearance, immunological modulation, vascularization, and osteogenesis. Based on the theory that bone healing is regulated by both biochemical and biophysical signals, in this study, a copper doped bioglass (CuBGs)/methacryloyl-modified gelatin nanoparticle (MA-GNPs)/methacrylated silk fibroin (SilMA) hybrid hydrogel is developed to promote IBD healing. This hybrid hydrogel demonstrates a dual-photocrosslinked interpenetrating network mechanism, wherein the photocrosslinked SilMA as the main network ensures structural integrity, and the photocrosslinked MA-GNPs colloidal network increases strength and dissipates loading forces. In an IBD model, the hydrogel exhibits excellent biophysical characteristics, such as adhesion, adaptation to irregular defect shapes, and in situ physical reinforcement. At the same time, by sequentially releasing bioactive ions such as Cu2+ , Ca2+ , and Si2+ ions from CuBGs on demand, the hydrogel spatiotemporally coordinates antibacterial, immunomodulatory and bone remodeling events, efficiently removing infection and accelerating bone repair without the use of antibiotics or exogenous recombinant proteins. Therefore, the hybrid hydrogel can be used as a simple and effective method for the treatment of IBD.
An invited commentary on ‘Survival outcomes of neoadjuvant therapy followed by radical resection versus upfront surgery for stage I-III pancreatic ductal adenocarcinoma: a retrospective cohort study’
Authors: Alessandro Coppola, Immacolata Iannone, Paolo Sapienza
Journal: International Journal of Surgery (2023)

Coppola, Alessandro MD, PhD, FACS, FEBS; Iannone, Immacolata; Sapienza, Paolo Author Information
A commentary on ‘Significance of anatomical resection and resection margin status in patients with HBV-related hepatocellular carcinoma and microvascular invasion: a multicenter propensity score-matched study’
Authors: Shiye Yang, Chunqiu Xia, Zhibing Ming
Journal: International Journal of Surgery (2023)

Department of Vascular Surgery, Nantong First People's Hospital, The Second Affiliated Hospital of Nantong University, 666 Shengli Road, Chongchuan District, Nantong City, Jiangsu Province 226014, China *Corresponding author. Address: Nantong First People's Hospital, The Second Affiliated Hospital of Nantong University, 666 Shengli Road, Chongchuan District, Nantong City, Jiangsu Province 226014, China. E-mail address: [email protected] (S. Yang) Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/
A commentary on ‘Detection of cancer cells and tumor margins during colorectal cancer surgery by intraoperative flow cytometry’
Authors: Yuan Chen, Chengcheng Wang, Yupei Zhao
Journal: International Journal of Surgery (2023)

Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100023, PR China Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ *Corresponding author. Address: Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100023, PR China. E-mail address: [email protected] (Y. Zhao). This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc/4.0/
A Bioglass‐Poly(lactic<i>‐co‐</i>glycolic Acid) Scaffold@Fibrin Hydrogel Construct to Support Endochondral Bone Formation
Authors: Dhanalakshmi Jeyachandran, Monzur Murshed, Lisbet Haglund, Marta Cerruti
Journal: Advanced Healthcare Materials (2023)

Bone tissue engineering using stem cells to build bone directly on a scaffold matrix often fails due to lack of oxygen at the injury site. This may be avoided by following the endochondral ossification route; herein, a cartilage template is promoted first, which can survive hypoxic environments, followed by its hypertrophy and ossification. However, hypertrophy is so far only achieved using biological factors. This work introduces a Bioglass-Poly(lactic-co-glycolic acid@fibrin (Bg-PLGA@fibrin) construct where a fibrin hydrogel infiltrates and encapsulates a porous Bg-PLGA. The hypothesis is that mesenchymal stem cells (MSCs) loaded in the fibrin gel and induced into chondrogenesis degrade the gel and become hypertrophic upon reaching the stiffer, bioactive Bg-PLGA core, without external induction factors. Results show that Bg-PLGA@fibrin induces hypertrophy, as well as matrix mineralization and osteogenesis; it also promotes a change in morphology of the MSCs at the gel/scaffold interface, possibly a sign of osteoblast-like differentiation of hypertrophic chondrocytes. Thus, the Bg-PLGA@fibrin construct can sequentially support the different phases of endochondral ossification purely based on material cues. This may facilitate clinical translation by decreasing in-vitro cell culture time pre-implantation and the complexity associated with the use of external induction factors.